popup improvements, citation fix

build/Citations.hs

@@ -139,14 +139,16 @@ transformInline keyNums (Cite citations _) =
         nums = mapMaybe (`Map.lookup` keyNums) keys
     in if null nums
            then Str ""
-           else RawInline "html" (markerHtml (head keys) (head nums) nums)
+           else RawInline "html" (markerHtml keys (head keys) (head nums) nums)
 transformInline _ x = x
 
-markerHtml :: Text -> Int -> [Int] -> Text
+markerHtml :: [Text] -> Text -> Int -> [Int] -> Text
-markerHtml firstKey firstNum nums =
+markerHtml keys firstKey firstNum nums =
     let label   = "[" <> T.intercalate "," (map tshow nums) <> "]"
+        allIds  = T.intercalate " " (map ("ref-" <>) keys)
     in "<sup class=\"cite-marker\" id=\"cite-back-" <> tshow firstNum <> "\">"
-    <> "<a href=\"#ref-" <> firstKey <> "\" class=\"cite-link\">"
+    <> "<a href=\"#ref-" <> firstKey <> "\" class=\"cite-link\""
+    <> " data-cite-keys=\"" <> allIds <> "\">"
     <> label <> "</a></sup>"
   where tshow = T.pack . show
 
@@ -196,10 +198,10 @@ entryOrder _ _ = maxBound
 
 -- | Prepend [N] marker to a bibliography entry block.
 addNumber :: Int -> Block -> Block
-addNumber n (Div attrs content) =
+addNumber n (Div attrs@(divId, _, _) content) =
     Div attrs
         ( Plain [ RawInline "html"
-                    ("<span class=\"ref-num\">[" <> T.pack (show n) <> "]</span>") ]
+                    ("<a class=\"ref-num\" href=\"#" <> divId <> "\">[" <> T.pack (show n) <> "]</a>") ]
           : content )
 addNumber _ b = b
 

cabal.project.freeze

@@ -49,7 +49,7 @@ constraints: any.Glob ==0.10.2,
              any.conduit ==1.3.6.1,
              any.conduit-extra ==1.3.8,
              any.containers ==0.6.7,
-             any.contravariant ==1.5.5,
+             any.contravariant ==1.5.6,
              any.cookie ==0.5.0,
              any.crypton ==1.0.4,
              any.crypton-connection ==0.4.5,
@@ -113,7 +113,7 @@ constraints: any.Glob ==0.10.2,
              any.lifted-base ==0.2.3.12,
              any.lrucache ==1.2.0.1,
              any.memory ==0.18.0,
-             any.mime-types ==0.1.2.0,
+             any.mime-types ==0.1.2.1,
              any.monad-control ==1.0.3.1,
              any.monad-logger ==0.3.42,
              monad-logger +template_haskell,
@@ -142,7 +142,7 @@ constraints: any.Glob ==0.10.2,
              any.prettyprinter-ansi-terminal ==1.1.3,
              any.primitive ==0.9.1.0,
              any.process ==1.6.19.0,
-             any.psqueues ==0.2.8.2,
+             any.psqueues ==0.2.8.3,
              any.random ==1.2.1.3,
              any.recv ==0.1.1,
              any.regex-base ==0.94.0.3,
@@ -153,7 +153,7 @@ constraints: any.Glob ==0.10.2,
              any.rts ==1.0.2,
              any.safe ==0.3.21,
              any.safe-exceptions ==0.1.7.4,
-             any.scientific ==0.3.8.0,
+             any.scientific ==0.3.8.1,
              any.semialign ==1.3.1,
              any.semigroupoids ==6.0.2,
              any.serialise ==0.2.6.1,
@@ -215,7 +215,7 @@ constraints: any.Glob ==0.10.2,
              any.unordered-containers ==0.2.20.1,
              any.utf8-string ==1.0.2,
              any.uuid-types ==1.0.6,
-             any.vault ==0.3.1.5,
+             any.vault ==0.3.1.6,
              any.vector ==0.13.2.0,
              any.vector-algorithms ==0.9.1.0,
              any.vector-stream ==0.1.0.1,

data/bibliography.bib

@@ -197,3 +197,285 @@
   year      = {2022},
   publisher = {University of Chicago Press}
 }
+
+% ── ICD Embeddings Preprint ─────────────────────────────────────────────────
+
+@misc{cms_hrrp,
+  author       = {{Centers for Medicare \& Medicaid Services}},
+  title        = {Hospital Readmissions Reduction Program ({HRRP})},
+  url          = {https://www.cms.gov/medicare/payment/prospective-payment-systems/acute-inpatient-pps/hospital-readmissions-reduction-program-hrrp}
+}
+
+@article{charlson1987,
+  author  = {Charlson, M. E. and Pompei, P. and Ales, K. L. and MacKenzie, C. R.},
+  title   = {A new method of classifying prognostic comorbidity in longitudinal studies: development and validation},
+  journal = {Journal of Chronic Diseases},
+  year    = {1987},
+  volume  = {40},
+  number  = {5},
+  pages   = {373--383}
+}
+
+@article{elixhauser1998,
+  author  = {Elixhauser, A. and Steiner, C. and Harris, D. R. and Coffey, R. M.},
+  title   = {Comorbidity measures for use with administrative data},
+  journal = {Medical Care},
+  year    = {1998},
+  volume  = {36},
+  number  = {1},
+  pages   = {8--27}
+}
+
+@article{deschepper2020,
+  author  = {Deschepper, Mathieu and Eeckloo, Kristof and Vogelaers, Dominique and Waegeman, Willem},
+  title   = {Using structured pathology data to predict hospital-wide mortality at admission},
+  journal = {PLoS One},
+  year    = {2020},
+  volume  = {15},
+  number  = {6},
+  pages   = {e0235117}
+}
+
+@article{lelay2022,
+  author  = {Le Lay, Jonathan and Martin, Sylvain and Mosnier, Arnaud and others},
+  title   = {Prediction of hospital readmission of multimorbid patients using machine learning models},
+  journal = {PLoS One},
+  year    = {2022},
+  volume  = {17},
+  number  = {12},
+  pages   = {e0279433}
+}
+
+@article{qiao2022,
+  author  = {Qiao, Edmund M. and Deng, Jie and Kluger, Harvey M. and Yu, James B. and Gross, Cary P.},
+  title   = {Evaluating High-Dimensional Machine Learning Models to Predict Hospital Mortality Among Older Patients With Cancer},
+  journal = {JCO Clinical Cancer Informatics},
+  year    = {2022},
+  volume  = {6},
+  pages   = {e2100186}
+}
+
+@article{davis2022,
+  author  = {Davis, Steve and Borah, Michael F. and Hansen, Justin and Malin, Bradley and Robinson, Jonathan and Turchin, Alexander},
+  title   = {Effective hospital readmission prediction models using machine-learned features},
+  journal = {BMC Health Services Research},
+  year    = {2022},
+  volume  = {22},
+  number  = {1},
+  pages   = {1415}
+}
+
+@article{harerimana2021,
+  author  = {Harerimana, Gaspard and Kim, Jong Wook and Jang, Beakcheol},
+  title   = {A deep attention model to forecast the Length Of Stay and the in-hospital mortality right on admission from {ICD} codes and demographic data},
+  journal = {Journal of Biomedical Informatics},
+  year    = {2021},
+  volume  = {118},
+  pages   = {103778}
+}
+
+@article{matsui2022,
+  author  = {Matsui, Hiroki and Yasunaga, Hideo and Fushimi, Kiyohide and Homma, Yuichi},
+  title   = {Development of Deep Learning Models for Predicting In-Hospital Mortality Using an Administrative Claims Database: Retrospective Cohort Study},
+  journal = {JMIR Medical Informatics},
+  year    = {2022},
+  volume  = {10},
+  number  = {2},
+  pages   = {e27936}
+}
+
+@article{nguyen2017,
+  author  = {Nguyen, Phuoc and Tran, Truyen and Wickramasinghe, Nilmini and Venkatesh, Svetha},
+  title   = {{Deepr}: A Convolutional Net for Medical Records},
+  journal = {IEEE Journal of Biomedical and Health Informatics},
+  year    = {2017},
+  volume  = {21},
+  number  = {1},
+  pages   = {22--30}
+}
+
+@misc{ahrq_elixhauser,
+  author = {{Agency for Healthcare Research and Quality}},
+  title  = {Elixhauser Comorbidity Software Refined for {ICD-10-CM}},
+  url    = {https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp}
+}
+
+@article{fernando2019,
+  author  = {Fernando, Dulith T. and Berecki-Gisolf, Janneke and Newstead, Stuart and Ansari, Zul},
+  title   = {Effect of comorbidity on injury outcomes: a review of existing indices},
+  journal = {Annals of Epidemiology},
+  year    = {2019},
+  volume  = {36},
+  pages   = {5--14}
+}
+
+@article{quan2005,
+  author  = {Quan, Hude and Sundararajan, Vijaya and Halfon, Patricia and others},
+  title   = {Coding algorithms for defining comorbidities in {ICD-9-CM} and {ICD-10} administrative data},
+  journal = {Medical Care},
+  year    = {2005},
+  volume  = {43},
+  number  = {11},
+  pages   = {1130--1139}
+}
+
+@article{deyo1992,
+  author  = {Deyo, Richard A. and Cherkin, Daniel C. and Ciol, Marcia A.},
+  title   = {Adapting a clinical comorbidity index for use with {ICD-9-CM} administrative databases},
+  journal = {Journal of Clinical Epidemiology},
+  year    = {1992},
+  volume  = {45},
+  number  = {6},
+  pages   = {613--619}
+}
+
+@article{quan2011,
+  author  = {Quan, Hude and Li, Bing and Couris, Chantal M. and others},
+  title   = {Updating and validating the {Charlson} comorbidity index and score for risk adjustment in hospital discharge abstracts using data from 6 countries},
+  journal = {American Journal of Epidemiology},
+  year    = {2011},
+  volume  = {173},
+  number  = {6},
+  pages   = {676--682}
+}
+
+@misc{stagg2006,
+  author    = {Stagg, Vince},
+  title     = {{CHARLSON}: {Stata} module to calculate {Charlson} index of comorbidity},
+  year      = {2006},
+  publisher = {Boston College Department of Economics}
+}
+
+@inproceedings{zaheer2017,
+  author    = {Zaheer, Manzil and Kottur, Satwik and Ravanbakhsh, Siamak and Poczos, Barnabas and Salakhutdinov, Ruslan and Smola, Alexander},
+  title     = {Deep Sets},
+  booktitle = {Advances in Neural Information Processing Systems},
+  year      = {2017},
+  volume    = {30}
+}
+
+@inproceedings{abadi2016,
+  author    = {Abadi, Mart{\'i}n and Barham, Paul and Chen, Jianmin and others},
+  title     = {{TensorFlow}: A System for Large-Scale Machine Learning},
+  booktitle = {Proceedings of the 12th {USENIX} Symposium on Operating Systems Design and Implementation},
+  year      = {2016},
+  pages     = {265--283}
+}
+
+@article{youden1950,
+  author  = {Youden, W. J.},
+  title   = {Index for rating diagnostic tests},
+  journal = {Cancer},
+  year    = {1950},
+  volume  = {3},
+  number  = {1},
+  pages   = {32--35}
+}
+
+@article{delong1988,
+  author  = {DeLong, Elizabeth R. and DeLong, David M. and Clarke-Pearson, Daniel L.},
+  title   = {Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach},
+  journal = {Biometrics},
+  year    = {1988},
+  volume  = {44},
+  number  = {3},
+  pages   = {837--845}
+}
+
+@inproceedings{sundararajan2017,
+  author    = {Sundararajan, Mukund and Taly, Ankur and Yan, Qiqi},
+  title     = {Axiomatic Attribution for Deep Networks},
+  booktitle = {Proceedings of the 34th International Conference on Machine Learning},
+  year      = {2017},
+  pages     = {3319--3328}
+}
+
+@article{joynt2013,
+  author  = {Joynt, Karen E. and Jha, Ashish K.},
+  title   = {Characteristics of hospitals receiving penalties under the {Hospital Readmissions Reduction Program}},
+  journal = {JAMA},
+  year    = {2013},
+  volume  = {309},
+  number  = {4},
+  pages   = {342--343}
+}
+
+@article{desai2016,
+  author  = {Desai, Nihar R. and Ross, Joseph S. and Kwon, Jin Yul and others},
+  title   = {Association Between Hospital Penalty Status Under the {Hospital Readmission Reduction Program} and Readmission Rates for Target and Nontarget Conditions},
+  journal = {JAMA},
+  year    = {2016},
+  volume  = {316},
+  number  = {24},
+  pages   = {2647--2656}
+}
+
+@article{zuckerman2017,
+  author  = {Zuckerman, Rachael B. and Sheingold, Steven H. and Orav, E. John and Ruhter, Jordan and Epstein, Arnold M.},
+  title   = {Effect of a Hospital-wide Measure on the Readmissions Reduction Program},
+  journal = {New England Journal of Medicine},
+  year    = {2017},
+  volume  = {377},
+  number  = {16},
+  pages   = {1551--1558}
+}
+
+@article{obermeyer2019,
+  author  = {Obermeyer, Ziad and Powers, Brian and Vogeli, Christine and Mullainathan, Sendhil},
+  title   = {Dissecting racial bias in an algorithm used to manage the health of populations},
+  journal = {Science},
+  year    = {2019},
+  volume  = {366},
+  number  = {6464},
+  pages   = {447--453}
+}
+
+@article{kind2014,
+  author  = {Kind, Amy J. H. and Jencks, Stephen and Brock, Jim and others},
+  title   = {Neighborhood socioeconomic disadvantage and 30-day rehospitalization: a retrospective cohort study},
+  journal = {Annals of Internal Medicine},
+  year    = {2014},
+  volume  = {161},
+  number  = {11},
+  pages   = {765--774}
+}
+
+@article{joynt2011,
+  author  = {Joynt, Karen E. and Orav, E. John and Jha, Ashish K.},
+  title   = {Thirty-day readmission rates for {Medicare} beneficiaries by race and site of care},
+  journal = {JAMA},
+  year    = {2011},
+  volume  = {305},
+  number  = {7},
+  pages   = {675--681}
+}
+
+@article{hansen2011,
+  author  = {Hansen, Luke O. and Young, Robert S. and Hinami, Keiki and Leung, Albert and Williams, Mark V.},
+  title   = {Interventions to reduce 30-day rehospitalization: a systematic review},
+  journal = {Annals of Internal Medicine},
+  year    = {2011},
+  volume  = {155},
+  number  = {8},
+  pages   = {520--528}
+}
+
+@article{coleman2006,
+  author  = {Coleman, Eric A. and Parry, Carla and Chalmers, Sandra and Min, Sung-joon},
+  title   = {The care transitions intervention: results of a randomized controlled trial},
+  journal = {Archives of Internal Medicine},
+  year    = {2006},
+  volume  = {166},
+  number  = {17},
+  pages   = {1822--1828}
+}
+
+@article{rudin2019,
+  author  = {Rudin, Cynthia},
+  title   = {Stop Explaining Black Box Machine Learning Models for High Stakes Decisions and Use Interpretable Models Instead},
+  journal = {Nature Machine Intelligence},
+  year    = {2019},
+  volume  = {1},
+  number  = {5},
+  pages   = {206--215}
+}

static/css/popups.css

@@ -83,6 +83,16 @@
    Shows the .csl-entry from the bibliography in-page.
    ============================================================ */
 
+.popup-citation-entry {
+    display: block;
+}
+
+.popup-citation-entry + .popup-citation-entry {
+    margin-top: 0.55rem;
+    padding-top: 0.55rem;
+    border-top: 1px solid var(--border);
+}
+
 .popup-citation .csl-entry {
     font-family: var(--font-sans);
     font-size: 0.8rem;
@@ -99,9 +109,16 @@
     word-break: break-all;
 }
 
-/* Hide the [N] number badge — already shown in the inline marker */
 .popup-citation .ref-num {
-    display: none;
+    font-weight: 600;
+    color: var(--text-faint);
+    margin-right: 0.35em;
+    font-variant-numeric: tabular-nums;
+    text-decoration: none;
+}
+
+.popup-citation .ref-num:hover {
+    color: var(--text);
 }
 
 /* Epistemic preview popup — content cloned from #epistemic; ep-* styles inherited */

static/js/popups.js

@@ -203,13 +203,20 @@
         );
     }
 
-    /* 1. Citations — synchronous DOM lookup */
+    /* 1. Citations — synchronous DOM lookup; supports multi-citation groups
+          via data-cite-keys (space-separated list of ref-* IDs). */
     function citationContent(target) {
         return new Promise(function (resolve) {
-            var id    = (target.getAttribute('href') || '').slice(1);
+            var keysAttr = target.getAttribute('data-cite-keys');
+            var ids = keysAttr
+                ? keysAttr.trim().split(/\s+/)
+                : [(target.getAttribute('href') || '').slice(1)];
+            var parts = ids.map(function (id) {
                 var entry = document.getElementById(id);
-            resolve(entry
+                return entry ? '<div class="popup-citation-entry">' + entry.innerHTML + '</div>' : null;
-                ? '<div class="popup-citation">' + entry.innerHTML + '</div>'
+            }).filter(Boolean);
+            resolve(parts.length
+                ? '<div class="popup-citation">' + parts.join('') + '</div>'
                 : null);
         });
     }

templates/partials/head.html

@@ -28,9 +28,6 @@ $if(search)$
 <link rel="stylesheet" href="/pagefind/pagefind-ui.css">
 $endif$
 <script src="/js/theme.js"></script>
-$if(has-citations)$
-<script src="/js/citations.js" defer></script>
-$endif$
 $if(viz)$
 <link rel="stylesheet" href="/css/viz.css">
 <script src="https://cdn.jsdelivr.net/npm/vega@5" defer></script>